Borrowing it
Nothing to install: this file belongs to broadinstitute/viral-ngs. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/broadinstitute/viral-ngs/main/AGENTS.mdgit clone --depth 1 https://github.com/broadinstitute/viral-ngsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/instructions/broadinstitute/viral-ngs/agents-md)<a href="https://agentmods.dev/instructions/broadinstitute/viral-ngs/agents-md"><img src="https://agentmods.dev/badge/instructions/broadinstitute/viral-ngs/agents-md/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/instructions/broadinstitute/viral-ngs/agents-md"><img src="https://agentmods.dev/badge/instructions/broadinstitute/viral-ngs/agents-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.05362 | $0.05362 |
| Opus 5 | $0.02681 | $0.02681 |
| Sonnet 5 | $0.01072 | $0.01072 |
| Haiku 4.5 | $0.00536 | $0.00536 |
Grade A, and why
viral-ngs AGENTS.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 5d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 610 lines — stays where its author put it; the contents beside it link to each section on GitHub.
AGENTS.md
This document provides guidance for AI assistants (Claude Code, GitHub Copilot, etc.) working on this repository.
Overview
viral-ngs is a consolidated monorepo for viral NGS (Next-Generation Sequencing) analysis tools. It provides:
- Core utilities: Read manipulation, Illumina demultiplexing, file handling, QC
- Assembly: Genome assembly, scaffolding, gap filling
- Classification: Metagenomic classification, taxonomy filtering, k-mer analysis
- Phylogenetics: Variant calling, consensus generation, annotation
Related resources:
- Command-line documentation: https://viral-ngs.readthedocs.org/
- Higher-level pipelines: https://github.com/broadinstitute/viral-pipelines
Development Environment
Docker-Centric Development
Development is intentionally docker-centric. Developers need:
- Docker
- Git
- Text/code editor
Development Workflow
-
Clone the repository:
git clone https://github.com/broadinstitute/viral-ngs.git -
Run the container with local checkout mounted:
docker run -it --rm \ -v $(pwd):/opt/viral-ngs/source \ quay.io/broadinstitute/viral-ngs:main-core -
If modifying conda dependencies, install them inside the container:
micromamba install <packages> -
Test code interactively:
cd /opt/viral-ngs/source pytest -rsxX -n auto tests/unit -
Push changes to GitHub for automated CI testing
Running Tests
# Run all unit tests in the core image
docker run --rm \
-v $(pwd):/opt/viral-ngs/source \
quay.io/broadinstitute/viral-ngs:main-core \
pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit
# Run specific module tests
docker run --rm \
-v $(pwd):/opt/viral-ngs/source \
quay.io/broadinstitute/viral-ngs:main-classify \
pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit/classify
Important: Testing source code changes requires re-installing the package.
The -v mount makes your local files visible on disk, but viral_ngs is already installed as a package inside the container image. Python imports resolve to the installed copy, not your mounted source files. If you've modified files under src/viral_ngs/, you must re-install before running tests:
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 5d ago Changed · +4 tokens per session 4e2714952441
- 9d ago First seen · 610 lines · 5,358 tokens per session scan A d17caefa5790
viral-ngs AGENTS.md is an instructions file published in the GitHub repository broadinstitute/viral-ngs (197 stars, last pushed 5d ago), licensed MIT. It adds 5,362 tokens to every session, about $0.0268 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other instructions, from other repositories
next.js AGENTS.md
AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.
codex AGENTS.md
AGENTS.md instructions for openai/codex, covering rust/codex-rs, the codex-core crate, code review rules, crate api surface and model visible context.
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, applying the notice (cutover) and fallback chain (never fail the build).
langchain AGENTS.md
AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.
deepseek-harness AGENTS.md
AGENTS.md instructions for deepseek-ai/deepseek-harness, covering agents.md, pre-stable apis and released session data, repository layout, commands and host sandbox failures.